Show Example Input
# Example input for a typical analysis run: path = "D:\jeries\output\TASC_pickles\" ST = "rawdata.pickle" STgraph = "rawdatagraph.pickle" MorphoFeatures = ['Area', 'Ellip_Ax_B_X', 'Ellip_Ax_B_Y'] BpwFeatures = ['Velocity_Full_Width_Half_Maximum', 'Velocity_Maximum_Height'] SAMPLE = False expList = [16,17,18,19,20,21,22,23] CellSample = 2 expListT = [0,1,2,3,4,5,6,7,8,9,10,11] title = "jeries_test" k_cluster = 3 MorphoOut = False MorphoIn = False combin = [["NNIR"],["METR"],["GABY"]] singleTREAT = False singleCONTROL = True multipleCL = False nrows = 1 ncols = 12 nColor = 12 nShades = 2 nColorTreat = 0 nShadesTreat = 0 nColorLay = 3 nShadesLay = 3 figsizeEXP = (25,5) figsizeTREATS = (15,5) figsizeCL = (15,15) CON = ['NNIR'] CL = ['293T'] wellCON = ['AM001100425CHR2B02293TNNIRNOCOWH00'] controls = [] summary_dir_path = "D:\jeries\output"
Sampling
If you want to sample cells to balance well sizes, check this box.
expList: Indices of wells to sample (comma-separated).CellSample: Sampling divisor (e.g., 2 for half, 3 for a third).Experiments to analyze (without sampling)
Indices for the wells you wish to analyze without sampling.
You can use a comma-separated list (e.g., 0,1,2,3,4,5,6,7,8,9,10,11) or a Python range (e.g., range(0,12)).
Experiment title and number of clusters
Choose a unique title for this run. All output files will use this as a prefix.
Set the number of clusters for k-means analysis.
Feature selection
Check to analyze only kinetics (BPW) or only morphology.
If you wish to run on the entire feature list, leave both unchecked.
Treatments Combination
Specify how your treatments can be combined in your experiments.
Example:
If your treatments are HGF2, HGF7, DOX1, PHA4, PHA3:
HGF2, HGF7, and DOX1 are not combined with each other, put them in the same list: ['HGF2', 'HGF7', 'DOX1']PHA4 and PHA3 are not combined with the others, put them in another list: ['PHA4', 'PHA3'][['HGF2', 'HGF7', 'DOX1'], ['PHA4', 'PHA3']]You will not find a well named 'HGF2HGF7' or 'HGF2DOX1', but you may find 'HGF7PHA4'.
Note:
If you have a control well (e.g., 'CON'), do not include it in any list.
Single/multiple treatment/control/cell lines
singleTREAT: True if only one treatment.singleCONTROL: True if only one control.multipleCL: True if multiple cell lines.Graph Properties
These settings control the appearance and layout of your output figures. You may need to adjust them depending on your experiment and preferences.
nrows, ncols:
Set the number of rows and columns in your experiment figures. For example, if you have 3 cell lines and 8 treatments, use nrows=3 and ncols=8.
Default: nrows=0, ncols=1
nColor, nShades:
Define the number of colors and shades used in the experiment figures.
Default: nColor=0, nShades=0
nColorTreat, nShadesTreat:
Number of colors and shades for treatment-specific figures. Usually, you can leave these at their default values.
Default: nColorTreat=0, nShadesTreat=0
nColorLay, nShadesLay:
Number of colors and shades for y-position (layer) figures.
Example: nColorLay=3, nShadesLay=3
figsizeEXP, figsizeTREATS, figsizeCL:
Set the figure size for experiment, treatment, and cell line figures as (width, height) tuples.
Example:
figsizeEXP = (40, 15)figsizeTREATS = (30, 15)figsizeCL = (15, 5)Tip: You may need to revisit and adjust these settings to get the best visualization for your data.
Chi-Squared Test Variables
CON:
List of control names (comma-separated).
Example: CON = ['CON'] or CON = ['CON1', 'CON2']
CL:
List of cell lines (comma-separated).
Example: CL = ['BT54', 'MDA2', 'MCF7'] or CL = ['293T']
wellCON:
List of well names for controls (one per line, without the 'NNN0' part).
Example:
HA033080917CHR1C02BT54CON0WH00 HA033080917CHR1D02MDA2CON0WH00 HA033080917CHR1F02MCF7CON0WH00
controls:
List of specific experiment names to use as controls (one per line).
Example:
BT54HGF7
Leave blank if not used.
✅ Found 12 summary files for 12 different wells
Analysis is running...
These are the unique experiment names found in your data:
If sampling is enabled, only a subset of cells from selected wells will be used. For example, CellSample=2 means every second cell track is sampled.
Sampling is disabled. All cells from selected wells will be used.
The following experiments will be analyzed (excluding sampled experiments if sampling is enabled):
expListT:
The experiment(s) you chose:
AM001100425CHR2B02293TNNIRNOCOWH00
AM001100425CHR2B03293TNNIRNOCOWH00
AM001100425CHR2B04293TNNIRNOCOWH00
AM001100425CHR2C02293TMETRNNIRNOCOWH00
AM001100425CHR2C03293TMETRNNIRNOCOWH00
AM001100425CHR2C04293TMETRNNIRNOCOWH00
AM001100425CHR2D02293TGABYNNIRNOCOWH00
AM001100425CHR2D03293TGABYNNIRNOCOWH00
AM001100425CHR2D04293TGABYNNIRNOCOWH00
AM001100425CHR2E02293TNNIRMETRGABYNOCOWH00
AM001100425CHR2E03293TNNIRMETRGABYNOCOWH00
AM001100425CHR2E04293TNNIRMETRGABYNOCOWH00
The cell line(s):
293T
293T
293T
293T
293T
293T
293T
293T
293T
293T
293T
293T
The treatments are:
Number of features: 49
The Features are:
There are 1 significant components
Treatments p-Value
Experiments p-Value AM001100425CHR2B02293TNNIRNOCOWH00
TimeLayers p-Value 0
Could not convert column: Experiment
Could not convert column: Treatments
Tukey combined table saved to: D:\jeries\TASC\TASC_streamlit_app\tukey_combined.xlsx
Analysis complete! You can rerun the analysis by clicking 'Run Analysis' again.